Cell Ranger ARC1.0, printed on 11/29/2023
Increases the upper limit on primary contigs (those that have at least one gene annotation) from 100 to 500. The pipeline will error out if more than 1000 total contigs are present in the reference.
Disables multithreading in mkref to address an issue where mkref would fail on hardware without AVX support. This will be fixed in a future release.
Creates cellranger-arc count for the analysis of 10x Chromium Single Cell Multiome ATAC + Gene Expression data generated from a single GEM well.
Creates cellranger-arc mkfastq for demultiplexing of ATAC or GEX flow cell data for analysis.
Creates cellranger-arc mkref to construct reference packages for use with cellranger-arc count starting with a reference FASTA file and a gene annotations GTF file.
Note: the software cannot be used for the analysis of 10x Chromium Single Cell ATAC, 10x Chromium Single Cell 3' Gene Expression data, or for any kind of joint analysis of the two.